Deer users
The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topol.top mdrun -s topol.tpr grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr mdrun -s md.tpr Whether the simulation iscorrect ?
ion.pdb
Description: Binary data
minim.mdp
Description: Binary data
nvt.mdp
Description: Binary data
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